• Animal cells and systems
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• 제12권4호
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• pp.261-267
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• 2008

The human chromosomes 2, 7, 12 and 17 show genomic homology around Hox gene clusters, is taken as evidence that these paralogous gene families might have arisen from a ancestral chromosomal segment through genome duplication events. We have examined protein data from vertebrate and invertebrate genomes to analyze the phylogenetic history of multi-gene families with three or more of their representatives linked to human Hox clusters. Topology comparison based upon statistical significance and information of chromosome location for these genes examined have revealed many of linked genes coduplicated with Hox gene clusters. Most linked genes to Hox clusters share the same evolutionary history and are duplicated in concert with each other. We conclude that gene families linked to Hox clusters may be suggestion of ancient genome duplications.

• Journal of Plant Biotechnology
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• 제7권1호
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• pp.17-25
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• 2005

We have mined each of the five A. thaliana chromosomes for the presence of simple sequence repeats (SSRs) and developed custom perl scripts to examine their distribution and abundance in relation to genomic position, local G/C content and location within and around transcribed sequences. The distribution of repeats and G/C content with respect to genomic regions (exons, UTRs, introns, intergenic regions and proximity to expressed genes) are shown. SSRs show a non-random distribution across the genome and a strong association within and around transcribed sequences, while G/C density is associated specifically with the coding portions of transcribed sequences. SSR motif repeat number shows a high degree of variation for each SSR type and a high degree of motif sequence bias reflecting local genome sequence composition. PCR primers suitable for the amplification of identified SSRs have been designed where possible, and are available for further studies.

• Genomics & Informatics
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• 제7권2호
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• pp.111-121
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• 2009

Cell membrane proteins play crucial roles in the cell's molecular interaction with its environment and within itself. They consist of membrane-bound proteins and many types of transmembrane (TM) proteins such as receptors, transporters, channel proteins, and enzymes. Membrane proteomes of cellular organisms reveal some characteristics in their global topological distribution according to their evolutionary positions, and show their own information transfer complexity. Predicted transmembrane segments (TMSs) in membrane proteomes with HMMTOP showed near power-law distribution and frequency characteristics in 6-TMS and 7-TMS proteins in prokaryotes and eukaryotes, respectively. This reaffirms the important roles of membrane receptors in cellular communication and biological evolutionary history.

• Tuberculosis and Respiratory Diseases
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• 제81권3호
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• pp.216-221
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• 2018

Background: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been challenging. Methods: WGS, annotation refinement, and orthology assignment for the GenBank accession number acquisition were performed on two clinical isolates from Chinese immigrants. In addition, the genomes of the two isolates were compared with the genomes of Mycobacterium tuberculosis isolates, from two native Korean and five native Chinese individuals using a phylogenetic topology tree based on the Multiple Alignment of Conserved Genomic Sequence with Rearrangements (Mauve) package. Results: The newly assigned accession numbers for two clinical isolates were CP020381.2 (a Korean-Chinese from Yanbian Province) and CP022014.1 (a Chinese from Shandong Province), respectively. Mauve alignment classified all nine TB isolates into a discriminative collinear set with matched regions. The phylogenetic analysis revealed a rooted phylogenetic tree grouping the nine strains into two lineages: strains from Chinese individuals and strains from Korean individuals. Conclusion: Phylogenetic trees based on the Mauve alignments were supposed to be useful in revealing the dynamics of TB transmission from immigrants in South Korea, which can provide valuable information for scaling up the TB screening policy for immigrants.

• Journal of Plant Biotechnology
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• 제49권3호
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• pp.171-177
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• 2022

The precise homeostatic regulation of local auxin accumulation in xylem precursors of cambium stem cell tissues is one of the most important mechanisms for plant vascular patterning and radial secondary growth. Walls are thin (WAT1), a novel intracellular auxin transporter, contributes directly to the auxin accumulation maxima in xylem precursors. According to recent research, the auxin signaling activated pathway-related gene network was significantly enriched during the secondary growth of Panax ginseng storage roots. These imply that during P. ginseng root secondary growth, specific signaling mechanisms for local auxin maxima in the vascular cambial cells are probably triggered. This study identified four WAT1-like genes, PgWAT1-1/-2 and PgWAT2-1/-2, in the P. ginseng genome. Their expression levels were greatly increased in nitratetreated storage roots stimulated for secondary root growth. PgWAT1-1 and PgWAT2-1 were similar to WAT1 from Arabidopsis and tomato plants in terms of their subcellular localization at a tonoplast and predicted transmembrane topology. We discovered that overexpression of PgWAT1-1 and PgWAT2-1 was sufficient to compensate for the secondary growth defects observed in slwat1-copi loss of function tomato mutants. This critical information from the PgWAT1-1 and PgWAT2-1 genes can potentially be used in future P. ginseng genetic engineering and breeding for increased crop yield.

• 미생물학회지
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• 제49권4호
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• pp.383-390
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• 2013

Vibrio cholerae균은 자연적으로 외부 유전자를 받아들이는 능력이 있으므로, 종간 수평적 유전자 전달 작용(LGT)을 받을 것으로 예상된다. 본 연구는 인체에 질병을 일으키는 3종의 비브리오균 사이에서 일어나는 LGT 현상의 정량적 측면들을 분석하였다. V. cholerae N16961, V. parahaemolyticus RIMD2210633, V. vulnificus CMCP6, Escherichia coli K12 substrain MG1655의 유전체 염기서열을 분석하여 4개의 유전체에 모두 존재하는 단백질 발현 유전자들의 4개 일조를 결정하였다. 각 조의 4개 유전자의 계통수를 작성하는 분석을 통하여, 다른 조들 간의 계통성의 일치성과 불일치성을 결정하고, 수직적 계통성과 수평적 계통성을 구분하였다. 약 70%의 조에서 계통수가 확정될 수 있었으며, 그 중 75%는 서로 일치하는 계통성을 보였고, 25%는 LGT 계통수를 보였다. 이 결과에 따르면, 비브리오균의 LGT는 다른 세균 분류균의 속보다는 과단위에서 발생하는 빈도의 LGT계통수를 보였다. 염색체별로 관찰하였을 때, 유전자 제공자별로 LGT가 집중되는 현상이 일부 관찰되었고, V. cholerae 균주의 작은 염색체에서는 염색체의 약 절반 길이에 해당하는 부분에서 제공자별 LGT 위치들이 집중되는 현상을 보였다. 이런 결과는 유전자 제공자에 따라 선택성이 반복적으로 작용하거나, 대규모의 LGT가 있다는 가설을 수립하게 하였으며, 유전자 제공자별로 LGT 유전형질이 선택성을 띄게 되는 원인과 그 현상이 비브리오균의 진화에 미치는 영향에 대한 연구의 필요성을 제시하였다.